[Bioperl-l] [Gmod-gbrowse] Bioperl 1.6 and Bio::Graphics

Scott Cain cain.cshl at gmail.com
Wed Nov 26 13:37:46 EST 2008

Hi Chris,

While the decision ultimately rests with Lincoln (as, presumably, will
most of the work :-)  I'm not sure I agree that the split needs to
happen before the 1.6 release.  Consider the case where GBrowse 1.70
requires a newer version of Bio::Graphics than is available in
BioPerl.  We would put a version requirement in the Makefile.PL for
Bio::Graphics::Panel to be some number greater than the current
BioPerl release and put it on cpan.  Users would then do the cpan
shell shuffle, and get the right version of Bio::Graphics, and if they
don't already have BioPerl, they'll get that too (with an older
version of Bio::Graphics that will be immediately overwritten).  Is
there a flaw (or horrible user experience) in my thinking?


On Wed, Nov 26, 2008 at 12:29 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Lincoln, Scott, (and anyone else interested),
> One of the items on the list for the next bioperl release is whether
> to split off Bio::Graphics before 1.6 roles out:
> http://www.bioperl.org/wiki/
> Talk:Release_1.6#Bio::Graphics_and_Splitting_BioPerl
> My general reasoning is that the Gbrowse devs can start releasing to
> CPAN on their own (bio-graphics specific) schedule and not be tied to
> the core release schedule.  bio-graphics would just be tied in to a
> minimally compatible CPAN bioperl-core release.  The link above
> elaborates more on the idea as well as potential issues (versioning,
> etc).
> We don't have to do it for this release, but my concern is if it
> doesn't happen prior to 1.6 it will have to wait until 1.7 (date
> unknown), thus further impeding a Gbrowse 2.0.  Therefore I think it's
> worth delaying 1.6 a couple weeks to see how this goes.  Any comments
> over the next week or two would be appreciated (gotta factor in the
> holiday break!).
> chris
> (I've set the reply-to for the bioperl list, so hopefully we won't get
> double posting to both lists for responses)
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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